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Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes

Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut m...

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Autores principales: Klimina, Ksenia M., Kasianov, Artem S., Poluektova, Elena U., Emelyanov, Kirill V., Voroshilova, Viktoriya N., Zakharevich, Natalia V., Kudryavtseva, Anna V., Makeev, Vsevolod J., Danilenko, Valery N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404652/
https://www.ncbi.nlm.nih.gov/pubmed/30863681
http://dx.doi.org/10.7717/peerj.6554
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author Klimina, Ksenia M.
Kasianov, Artem S.
Poluektova, Elena U.
Emelyanov, Kirill V.
Voroshilova, Viktoriya N.
Zakharevich, Natalia V.
Kudryavtseva, Anna V.
Makeev, Vsevolod J.
Danilenko, Valery N.
author_facet Klimina, Ksenia M.
Kasianov, Artem S.
Poluektova, Elena U.
Emelyanov, Kirill V.
Voroshilova, Viktoriya N.
Zakharevich, Natalia V.
Kudryavtseva, Anna V.
Makeev, Vsevolod J.
Danilenko, Valery N.
author_sort Klimina, Ksenia M.
collection PubMed
description Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.
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spelling pubmed-64046522019-03-12 Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes Klimina, Ksenia M. Kasianov, Artem S. Poluektova, Elena U. Emelyanov, Kirill V. Voroshilova, Viktoriya N. Zakharevich, Natalia V. Kudryavtseva, Anna V. Makeev, Vsevolod J. Danilenko, Valery N. PeerJ Bioinformatics Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes. PeerJ Inc. 2019-03-04 /pmc/articles/PMC6404652/ /pubmed/30863681 http://dx.doi.org/10.7717/peerj.6554 Text en © 2019 Klimina et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Klimina, Ksenia M.
Kasianov, Artem S.
Poluektova, Elena U.
Emelyanov, Kirill V.
Voroshilova, Viktoriya N.
Zakharevich, Natalia V.
Kudryavtseva, Anna V.
Makeev, Vsevolod J.
Danilenko, Valery N.
Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
title Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
title_full Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
title_fullStr Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
title_full_unstemmed Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
title_short Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
title_sort employing toxin-antitoxin genome markers for identification of bifidobacterium and lactobacillus strains in human metagenomes
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404652/
https://www.ncbi.nlm.nih.gov/pubmed/30863681
http://dx.doi.org/10.7717/peerj.6554
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